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@sanger-tol

Tree of Life programme

The Tree of Life Programme investigates the diversity of complex organisms (eukaryotes) through sequencing and cellular technology

Hello 👋 !

You can find here most of the production code used by the Tree of Life 🌍 programme at the Sanger Institute, including the suite of Nextflow pipelines ⚙️ we use to generate hundreds of high-quality reference genome assemblies.

We also use these organisations and repositories:

Visit our main website at https://pipelines.tol.sanger.ac.uk/ to learn more about our mission 🧑‍🚀 !

Popular repositories Loading

  1. PretextView PretextView Public

    OpenGL Powered Pretext Contact Map Viewer

    C 29 8

  2. genomenote genomenote Public

    This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.

    Python 24 6

  3. treeval treeval Public

    Pipelines for the production of Treeval data

    Nextflow 22 4

  4. PretextMap PretextMap Public

    Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.

    C 20 2

  5. genomeassembly genomeassembly Public

    Implementation of ToL genome assembly workflows

    Nextflow 20 2

  6. yahs yahs Public

    Forked from c-zhou/yahs

    Yet another Hi-C scaffolding tool

    C 19 4

Repositories

Showing 10 of 47 repositories
  • agp-tpf-utils Public

    Code for manipulating AGP and TPF assembly files

    sanger-tol/agp-tpf-utils’s past year of commit activity
    Python 2 MIT 1 3 0 Updated Nov 7, 2024
  • ascc Public

    A Nextflow DSL2 pipeline for the identification of cobiont and contaminating sequences using fasta and pacbio data.

    sanger-tol/ascc’s past year of commit activity
    Python 3 MIT 0 10 2 Updated Nov 7, 2024
  • nf-core-tools Public Forked from nf-core/tools

    Python package with helper tools for the nf-core community.

    sanger-tol/nf-core-tools’s past year of commit activity
    Python 0 MIT 190 4 2 Updated Nov 7, 2024
  • sanger-tol/rapid-curation’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Nov 6, 2024
  • genomeassembly Public

    Implementation of ToL genome assembly workflows

    sanger-tol/genomeassembly’s past year of commit activity
    Nextflow 20 MIT 2 7 2 Updated Nov 5, 2024
  • genomenote Public

    This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.

    sanger-tol/genomenote’s past year of commit activity
    Python 24 MIT 6 14 (1 issue needs help) 0 Updated Nov 4, 2024
  • blobtoolkit Public

    Nextflow pipeline for BlobToolKit for Sanger ToL production suite

    sanger-tol/blobtoolkit’s past year of commit activity
    Nextflow 11 MIT 2 5 2 Updated Nov 4, 2024
  • nf-core-website Public Forked from nf-core/website

    Code and files for the main nf-core website.

    sanger-tol/nf-core-website’s past year of commit activity
    Astro 0 MIT 194 0 0 Updated Oct 25, 2024
  • readmapping Public

    Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.

    sanger-tol/readmapping’s past year of commit activity
    Nextflow 10 MIT 7 14 2 Updated Oct 24, 2024
  • curationpretext Public

    A Nextflow DSL2 pipeline for pretext generation in curation

    sanger-tol/curationpretext’s past year of commit activity
    Nextflow 5 4 7 1 Updated Oct 24, 2024

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